def setup():
shared.setup()
global t_new, t_new_e, t_old, t_old_e, t_client_new, t_client_old
t_new = TaxonAPI(shared.services, shared.token, taxon_new)
t_new_e = _Taxon(shared.services, shared.token, taxon_new)
t_old = TaxonAPI(shared.services, shared.token, taxon_old)
t_old_e = _KBaseGenomes_Genome(shared.services, shared.token, taxon_old)
_log.info("Connecting to Taxon Thrift Service at {}".format(shared.services["taxon_service_url"]))
t_client_new = TaxonClientAPI(shared.services["taxon_service_url"], shared.token, taxon_new)
t_client_old = TaxonClientAPI(shared.services["taxon_service_url"], shared.token, taxon_old)
def test_api_service(service_name='assembly',apiurl='http://localhost',token=None):
try:
if service_name == "taxon":
#from doekbase.data_api.taxonomy.taxon.service import thrift_client
from doekbase.data_api.taxonomy.taxon.api import TaxonClientAPI
api = TaxonClientAPI(apiurl, token, 'ReferenceTaxons/242159_taxon')
elif service_name == "assembly":
#from doekbase.data_api.sequence.assembly.service import thrift_client
from doekbase.data_api.sequence.assembly.api import AssemblyClientAPI
api = AssemblyClientAPI(apiurl, token, 'ReferenceGenomeAnnotations/kb|g.166819_assembly')
elif service_name == "genome_annotation":
#from doekbase.data_api.annotation.genome_annotation.service import thrift_client
from doekbase.data_api.annotation.genome_annotation.api import GenomeAnnotationClientAPI
api = GenomeAnnotationClientAPI(apiurl, token, 'ReferenceGenomeAnnotations/kb|g.166819')
else:
raise Exception("Service not activated: {}".format(service_name))
except Exception as e:
print '3 ' + service_name + '_api - UNKNOWN - could not load client library for ' + service_name + ' ' + str(sys.path) + ' ' + str(sys.exc_info()[0])
raise
if service_name == 'genome_annotation':
try:
feature_types = api.get_feature_types()
if 'CDS' in feature_types:
print '0 ' + service_name + '_api - OK - feature_type returned ' + str(feature_types)
else:
print '2 ' + service_name + '_api - CRITICAL - unexpected feature_types returned ' + str(feature_types)
except:
print '2 ' + service_name + '_api - CRITICAL - unexpected error encountered ' + str(sys.exc_info()[0])
if service_name == 'taxon':
try:
lineage = api.get_scientific_lineage()
if 'Ostreococcus' in lineage:
print '0 ' + service_name + '_api - OK - expected lineage OK ' + str(lineage)
else:
print '2 ' + service_name + '_api - CRITICAL - unexpected lineage ' + str(lineage)
except:
print '2 ' + service_name + '_api - CRITICAL - unexpected error encountered ' + str(sys.exc_info()[0])
if service_name == 'assembly':
try:
stats = api.get_stats()
ref_num_contigs=21
if stats['num_contigs']==ref_num_contigs:
print '0 ' + service_name + '_api - OK - ' + str(ref_num_contigs) + ' contigs found'
else:
print '2 ' + service_name + '_api - CRITICAL - ' + str(stats['num_contigs']) + ' contigs found, not ' + str(ref_num_contigs)
except:
print '2 ' + service_name + '_api - CRITICAL - unexpected error encountered ' + str(sys.exc_info()[0])
def test_client():
ap = argparse.ArgumentParser()
ap.add_argument('--ref',
default='ReferenceTaxons/242159_taxon',
help='Object reference ID, e.g. 1019/4/1')
ap.add_argument('--url',
dest='url',
default='http://localhost:9101',
metavar='URL',
help='Remote server url '
'(default=%(default)s)')
args = ap.parse_args()
token = ''
if os.environ.has_key('KB_AUTH_TOKEN'):
token = os.environ['KB_AUTH_TOKEN']
api = TaxonClientAPI(args.url, token, args.ref)
print("Getting data..")
t0 = time.time()
object_info = api.get_info()
dt = time.time() - t0
print object_info
print("Got and parsed data from get_info in {:g} seconds".format(dt))
t0 = time.time()
history = api.get_history()
dt = time.time() - t0
print history
print("Got and parsed data from get_history in {:g} seconds".format(dt))
t0 = time.time()
provenance = api.get_provenance()
dt = time.time() - t0
print provenance
print("Got and parsed data from get_provenance in {:g} seconds".format(dt))
t0 = time.time()
id = api.get_id()
dt = time.time() - t0
print id
print("Got and parsed data from get_id in {:g} seconds".format(dt))
t0 = time.time()
name = api.get_name()
dt = time.time() - t0
print name
print("Got and parsed data from get_name in {:g} seconds".format(dt))
t0 = time.time()
version = api.get_version()
dt = time.time() - t0
print version
print("Got and parsed data from get_version in {:g} seconds".format(dt))
t0 = time.time()
genetic_code = api.get_genetic_code()
dt = time.time() - t0
print genetic_code
print(
"Got and parsed data from get_genetic_code in {:g} seconds".format(dt))
t0 = time.time()
aliases = api.get_aliases()
dt = time.time() - t0
print aliases
print("Got and parsed data from get_aliases in {:g} seconds".format(dt))
t0 = time.time()
domain = api.get_domain()
dt = time.time() - t0
print domain
print("Got and parsed data from get_domain in {:g} seconds".format(dt))
try:
t0 = time.time()
kingdom = api.get_kingdom()
dt = time.time() - t0
print kingdom
print(
"Got and parsed data from get_kingdom in {:g} seconds".format(dt))
except:
pass
t0 = time.time()
taxonomic_id = api.get_taxonomic_id()
dt = time.time() - t0
print taxonomic_id
print(
"Got and parsed data from get_taxonomic_id in {:g} seconds".format(dt))
t0 = time.time()
scientific_lineage = api.get_scientific_lineage()
dt = time.time() - t0
print scientific_lineage
print("Got and parsed data from get_scientific_lineage in {:g} seconds".
format(dt))
t0 = time.time()
genome_annotations = api.get_genome_annotations()
dt = time.time() - t0
print genome_annotations
print("Got and parsed data from get_genome_annotations in {:g} seconds".
format(dt))
t0 = time.time()
parent = api.get_parent()
dt = time.time() - t0
print parent
print("Got and parsed data from get_parent in {:g} seconds".format(dt))
t0 = time.time()
children = api.get_children()
dt = time.time() - t0
print children
print("Got and parsed data from get_children in {:g} seconds".format(dt))
def test_client():
ap = argparse.ArgumentParser()
ap.add_argument('--ref', default='ReferenceTaxons/242159_taxon', help='Object reference ID, e.g. 1019/4/1')
ap.add_argument('--url', dest='url', default='http://localhost:9101',
metavar='URL', help='Remote server url '
'(default=%(default)s)')
args = ap.parse_args()
token='';
if os.environ.has_key('KB_AUTH_TOKEN'):
token = os.environ['KB_AUTH_TOKEN']
api = TaxonClientAPI(args.url, token, args.ref)
print("Getting data..")
t0 = time.time()
object_info = api.get_info()
dt = time.time() - t0
print object_info
print("Got and parsed data from get_info in {:g} seconds".format(dt))
t0 = time.time()
history = api.get_history()
dt = time.time() - t0
print history
print("Got and parsed data from get_history in {:g} seconds".format(dt))
t0 = time.time()
provenance = api.get_provenance()
dt = time.time() - t0
print provenance
print("Got and parsed data from get_provenance in {:g} seconds".format(dt))
t0 = time.time()
id = api.get_id()
dt = time.time() - t0
print id
print("Got and parsed data from get_id in {:g} seconds".format(dt))
t0 = time.time()
name = api.get_name()
dt = time.time() - t0
print name
print("Got and parsed data from get_name in {:g} seconds".format(dt))
t0 = time.time()
version = api.get_version()
dt = time.time() - t0
print version
print("Got and parsed data from get_version in {:g} seconds".format(dt))
t0 = time.time()
genetic_code = api.get_genetic_code()
dt = time.time() - t0
print genetic_code
print("Got and parsed data from get_genetic_code in {:g} seconds".format(dt))
t0 = time.time()
aliases = api.get_aliases()
dt = time.time() - t0
print aliases
print("Got and parsed data from get_aliases in {:g} seconds".format(dt))
t0 = time.time()
domain = api.get_domain()
dt = time.time() - t0
print domain
print("Got and parsed data from get_domain in {:g} seconds".format(dt))
try:
t0 = time.time()
kingdom = api.get_kingdom()
dt = time.time() - t0
print kingdom
print("Got and parsed data from get_kingdom in {:g} seconds".format(dt))
except:
pass
t0 = time.time()
taxonomic_id = api.get_taxonomic_id()
dt = time.time() - t0
print taxonomic_id
print("Got and parsed data from get_taxonomic_id in {:g} seconds".format(dt))
t0 = time.time()
scientific_lineage = api.get_scientific_lineage()
dt = time.time() - t0
print scientific_lineage
print("Got and parsed data from get_scientific_lineage in {:g} seconds".format(dt))
t0 = time.time()
genome_annotations = api.get_genome_annotations()
dt = time.time() - t0
print genome_annotations
print("Got and parsed data from get_genome_annotations in {:g} seconds".format(dt))
t0 = time.time()
parent = api.get_parent()
dt = time.time() - t0
print parent
print("Got and parsed data from get_parent in {:g} seconds".format(dt))
t0 = time.time()
children = api.get_children()
dt = time.time() - t0
print children
print("Got and parsed data from get_children in {:g} seconds".format(dt))
def test_client():
ap = argparse.ArgumentParser()
ap.add_argument('--ref', default='ReferenceTaxons/83333_taxon', help='Object reference ID, e.g. 1019/4/1')
ap.add_argument('--host', dest='host', default='localhost',
metavar='ADDR', help='Remote server host '
'(default=%(default)s)')
ap.add_argument('--port', dest='port', default=9090,
metavar='PORT', help='Remote server port '
'(default=%(default)d)')
args = ap.parse_args()
api = TaxonClientAPI(args.host, args.port, os.environ["KB_AUTH_TOKEN"], args.ref)
print("Getting data..")
t0 = time.time()
genetic_code = api.get_genetic_code()
dt = time.time() - t0
print genetic_code
print("Got and parsed data in {:g} seconds".format(dt))
t0 = time.time()
aliases = api.get_aliases()
dt = time.time() - t0
print aliases
print("Got and parsed data in {:g} seconds".format(dt))
t0 = time.time()
domain = api.get_domain()
dt = time.time() - t0
print domain
print("Got and parsed data in {:g} seconds".format(dt))
try:
t0 = time.time()
kingdom = api.get_kingdom()
dt = time.time() - t0
print kingdom
print("Got and parsed data in {:g} seconds".format(dt))
except:
pass
t0 = time.time()
taxonomic_id = api.get_taxonomic_id()
dt = time.time() - t0
print taxonomic_id
print("Got and parsed data in {:g} seconds".format(dt))
t0 = time.time()
scientific_lineage = api.get_scientific_lineage()
dt = time.time() - t0
print scientific_lineage
print("Got and parsed data in {:g} seconds".format(dt))
t0 = time.time()
genome_annotations = api.get_genome_annotations()
dt = time.time() - t0
print genome_annotations
print("Got and parsed data in {:g} seconds".format(dt))
t0 = time.time()
parent = api.get_parent()
dt = time.time() - t0
print parent
print("Got and parsed data in {:g} seconds".format(dt))
t0 = time.time()
children = api.get_children()
dt = time.time() - t0
print children
print("Got and parsed data in {:g} seconds".format(dt))
def test_api_service(service_name='assembly',
apiurl='http://localhost',
token=None):
try:
if service_name == "taxon":
#from doekbase.data_api.taxonomy.taxon.service import thrift_client
from doekbase.data_api.taxonomy.taxon.api import TaxonClientAPI
api = TaxonClientAPI(apiurl, token, 'ReferenceTaxons/242159_taxon')
elif service_name == "assembly":
#from doekbase.data_api.sequence.assembly.service import thrift_client
from doekbase.data_api.sequence.assembly.api import AssemblyClientAPI
api = AssemblyClientAPI(
apiurl, token,
'ReferenceGenomeAnnotations/kb|g.166819_assembly')
elif service_name == "genome_annotation":
#from doekbase.data_api.annotation.genome_annotation.service import thrift_client
from doekbase.data_api.annotation.genome_annotation.api import GenomeAnnotationClientAPI
api = GenomeAnnotationClientAPI(
apiurl, token, 'ReferenceGenomeAnnotations/kb|g.166819')
else:
raise Exception("Service not activated: {}".format(service_name))
except Exception as e:
print '3 ' + service_name + '_api - UNKNOWN - could not load client library for ' + service_name + ' ' + str(
sys.path) + ' ' + str(sys.exc_info()[0])
raise
if service_name == 'genome_annotation':
try:
feature_types = api.get_feature_types()
if 'CDS' in feature_types:
print '0 ' + service_name + '_api - OK - feature_type returned ' + str(
feature_types)
else:
print '2 ' + service_name + '_api - CRITICAL - unexpected feature_types returned ' + str(
feature_types)
except:
print '2 ' + service_name + '_api - CRITICAL - unexpected error encountered ' + str(
sys.exc_info()[0])
if service_name == 'taxon':
try:
lineage = api.get_scientific_lineage()
if 'Ostreococcus' in lineage:
print '0 ' + service_name + '_api - OK - expected lineage OK ' + str(
lineage)
else:
print '2 ' + service_name + '_api - CRITICAL - unexpected lineage ' + str(
lineage)
except:
print '2 ' + service_name + '_api - CRITICAL - unexpected error encountered ' + str(
sys.exc_info()[0])
if service_name == 'assembly':
try:
stats = api.get_stats()
ref_num_contigs = 21
if stats['num_contigs'] == ref_num_contigs:
print '0 ' + service_name + '_api - OK - ' + str(
ref_num_contigs) + ' contigs found'
else:
print '2 ' + service_name + '_api - CRITICAL - ' + str(
stats['num_contigs']) + ' contigs found, not ' + str(
ref_num_contigs)
except:
print '2 ' + service_name + '_api - CRITICAL - unexpected error encountered ' + str(
sys.exc_info()[0])